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For each sample, we compute the average pairwise distance and compare this to the average pair distance of S. The rank of S in this distribution provides a p-value, which is significant if the vast bulk of random samples have greater pairwise distance than S. Results are shown in Figure 8.
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Comparisons of pairwise distances revealed that ZF domains of subsets C2 and C3 show greater pairwise distances than those of the families C1 and A1.
The greatest pairwise distance among the Ns-type sequences of Leymus ranged from 0.210 to 3.377%, while the greatest pairwise distance among the Xm-type sequences of Leymus ranged from 0.208 to 2.401%.
The greatest pairwise distances between any two beta and alpha tubulin protein sequences are 0.464 (Tcβ4 vs. Nvβ1) and 0.700 (Agα2 vs. Amα4) respectively, which reveals that a wide range of amino acid sequence identities are capable of supporting microtubule assembly per se (Tables 1, 2).
SNPs with a pairwise distance greater than 50 cM were excluded since estimates of average r at greater distances are close to 0, which would result in the correlation of LD phase to be close to 0 as well.
In order to obtain a non-redundant and representative set of NLPs, all sequences analyzed have a pairwise distance greater than 10%.
Specifically, assemblies were discarded from further analyses if they were estimated to be less than 80% complete, or if the pairwise distance to their subsectional assembly reference was greater than two times the standard deviation of all pairwise distances between assembled members of their subsection and the subsectional reference.
For both Acc1 and CEN, the analysis of pairwise distance between sequences from diploid samples failed to produce a p value of greater than 0.01.
A comparison of pairwise distance distribution functions and envelopes indicates that glycosylated Skp1 is elongated with a 13% larger volume, greater than the 4.6% Mr increment of the dimer.
On the basis of pairwise distance calculations alone, the evolutionary divergence between C. paramecium and G. theta/ R. salina was invariably greater than between G. theta and R. salina (supplementary table S1, Supplementary Material online).
Additional file 6 shows that nearly all Selaginella EXPA genes have their lowest pairwise distance to a member of Arabidopsis-rice clades I – IV, again potentially suggesting that they are under greater purifying selection.
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